Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome)
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A, Walther-Antonio MRS
Journal
Scientific reports
Year
2019
Incidence rates for endometrial cancer (EC) are rising, particularly in postmenopausal and obese women. Previously, we showed that the uterine and vaginal microbiome distinguishes patients with EC from those without. Here, we sought to examine the impact of patient factors (such as menopause status, body mass index, and vaginal pH) in the microbiome in the absence of EC and how these might contribute to the microbiome signature in EC. We find that each factor independently alters the microbiome and identified postmenopausal status as the main driver of a polymicrobial network associated with EC (ECbiome). We identified Porphyromas somerae presence as the most predictive microbial marker of EC and we confirm this using targeted qPCR, which could be of use in detecting EC in high-risk, asymptomatic women. Given the established pathogenic behavior of P. somerae and accompanying network in tissue infections and ulcers, future investigation into their role in EC is warranted.
Experiment 1
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Lower part of vagina Caudal vagina,Lower third of vagina,Lower vagina,Perineal part of vagina,Sinus vagina,Vagina lower part,Vaginal bulb,Lower part of vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- endometrial cancer cancer of endometrium,endometrial Ca,endometrial cancer,endometrial neoplasm,endometrium cancer,malignant endometrial neoplasm,malignant endometrium neoplasm,malignant neoplasm of endometrium,neoplasm of endometrium,primary malignant neoplasm of endometrium,tumor of endometrium
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients undergoing hysterectomy
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- vaginal pH, menopause, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Needs review
Source: Figure 2, Table S1
Description: Bacterial OTUs differentially enriched among patients without EC by menopause status
Abundance in Group 1: increased abundance in post
| NCBI | Links |
|---|---|
| candidate phylum NAG2 |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Figure 2, Table S1
Description: Bacterial OTUs differentially enriched among patients without EC by menopause status
Abundance in Group 1: decreased abundance in post
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Lower part of vagina Caudal vagina,Lower third of vagina,Lower vagina,Perineal part of vagina,Sinus vagina,Vagina lower part,Vaginal bulb,Lower part of vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- endometrial cancer cancer of endometrium,endometrial Ca,endometrial cancer,endometrial neoplasm,endometrium cancer,malignant endometrial neoplasm,malignant endometrium neoplasm,malignant neoplasm of endometrium,neoplasm of endometrium,primary malignant neoplasm of endometrium,tumor of endometrium
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- benign
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- endometrial cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients undergoing hysterectomy for endometrial cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 75
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- vaginal pH, Confounders controlled for: "menopause status and body mass index" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.menopause status and body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Figure 4
Description: Bacterial OTUs differentially enriched among patients with and without EC
Abundance in Group 1: increased abundance in endometrial cancer
| NCBI | Links |
|---|---|
| Anaerococcus ⚠ | |
| Lactobacillus |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Figure 4
Description: Bacterial OTUs differentially enriched among patients with and without EC
Abundance in Group 1: decreased abundance in endometrial cancer
| NCBI | Links |
|---|---|
| Lactobacillus | |
| Porphyromonas | |
| Prevotella | |
| Finegoldia | |
| Peptoniphilus ⚠ | |
| Fusobacterium | |
| Campylobacter | |
| Actinomyces | |
| Peptococcus | |
| Gallicola | |
| Varibaculum ⚠ | |
| Arcanobacterium ⚠ |
Revision editor(s): WikiWorks
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